Merge branch 'dev' into feature/organic-extraction

unilabos/devices/liquid_handling/liquid_handler_abstract.py

@@ -21,10 +21,21 @@ from pylabrobot.resources import (
     ResourceHolder,
     Lid,
     Trash,
-    Tip,
+    Tip, TubeRack,
 )
+from typing_extensions import TypedDict
+
+from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
+from unilabos.registry.placeholder_type import ResourceSlot
+from unilabos.resources.resource_tracker import (
+    ResourceTreeSet,
+    ResourceDict,
+    EXTRA_SAMPLE_UUID,
+    EXTRA_UNILABOS_SAMPLE_UUID,
+)
+from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode, ROS2DeviceNode
+
 
-from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
 class SimpleReturn(TypedDict):
     samples: List[List[ResourceDict]]
     volumes: List[float]
@@ -237,12 +248,11 @@ class LiquidHandlerMiddleware(LiquidHandler):
         res_samples = []
         res_volumes = []
         for resource, volume, channel in zip(resources, vols, use_channels):
-            res_samples.append(
-                {"name": resource.name, "sample_uuid": resource.unilabos_extra.get("sample_uuid", None)}
-            )
+            sample_uuid_value = resource.unilabos_extra.get(EXTRA_SAMPLE_UUID, None)
+            res_samples.append({"name": resource.name, EXTRA_SAMPLE_UUID: sample_uuid_value})
             res_volumes.append(volume)
             self.pending_liquids_dict[channel] = {
-                "sample_uuid": resource.unilabos_extra.get("sample_uuid", None),
+                EXTRA_SAMPLE_UUID: sample_uuid_value,
                 "volume": volume,
             }
         return SimpleReturn(samples=res_samples, volumes=res_volumes)
@@ -284,10 +294,10 @@ class LiquidHandlerMiddleware(LiquidHandler):
         res_samples = []
         res_volumes = []
         for resource, volume, channel in zip(resources, vols, use_channels):
-            res_uuid = self.pending_liquids_dict[channel]["sample_uuid"]
+            res_uuid = self.pending_liquids_dict[channel][EXTRA_SAMPLE_UUID]
             self.pending_liquids_dict[channel]["volume"] -= volume
-            resource.unilabos_extra["sample_uuid"] = res_uuid
-            res_samples.append({"name": resource.name, "sample_uuid": res_uuid})
+            resource.unilabos_extra[EXTRA_SAMPLE_UUID] = res_uuid
+            res_samples.append({"name": resource.name, EXTRA_SAMPLE_UUID: res_uuid})
             res_volumes.append(volume)
 
         return SimpleReturn(samples=res_samples, volumes=res_volumes)
@@ -687,7 +697,52 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
             well.set_liquids([(liquid_name, volume)])  # type: ignore
             res_volumes.append(volume)
 
-        return SimpleReturn(samples=res_samples, volumes=res_volumes)
+        return SetLiquidReturn(
+            wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), volumes=res_volumes  # type: ignore
+        )
+
+    def set_liquid_from_plate(
+        self, plate: ResourceSlot, well_names: list[str], liquid_names: list[str], volumes: list[float]
+    ) -> SetLiquidFromPlateReturn:
+        """Set the liquid in wells of a plate by well names (e.g., A1, A2, B3).
+
+        如果 liquid_names 和 volumes 为空，但 plate 和 well_names 不为空，直接返回 plate 和 wells。
+        """
+        assert issubclass(plate.__class__, Plate) or issubclass(plate.__class__, TubeRack) , f"plate must be a Plate, now: {type(plate)}"
+        plate: Union[Plate, TubeRack]
+        # 根据 well_names 获取对应的 Well 对象
+        if issubclass(plate.__class__, Plate):
+            wells = [plate.get_well(name) for name in well_names]
+        elif issubclass(plate.__class__, TubeRack):
+            wells = [plate.get_tube(name) for name in well_names]
+        res_volumes = []
+
+        # 如果 liquid_names 和 volumes 都为空，直接返回
+        if not liquid_names and not volumes:
+            return SetLiquidFromPlateReturn(
+                plate=ResourceTreeSet.from_plr_resources([plate], known_newly_created=False).dump(),  # type: ignore
+                wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(),  # type: ignore
+                volumes=res_volumes,
+            )
+
+        for well, liquid_name, volume in zip(wells, liquid_names, volumes):
+            well.set_liquids([(liquid_name, volume)])  # type: ignore
+            res_volumes.append(volume)
+
+        task = ROS2DeviceNode.run_async_func(self._ros_node.update_resource, True, **{"resources": wells})
+        submit_time = time.time()
+        while not task.done():
+            if time.time() - submit_time > 10:
+                self._ros_node.lab_logger().info(f"set_liquid_from_plate {plate} 超时")
+                break
+            time.sleep(0.01)
+
+        return SetLiquidFromPlateReturn(
+            plate=ResourceTreeSet.from_plr_resources([plate], known_newly_created=False).dump(),  # type: ignore
+            wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(),  # type: ignore
+            volumes=res_volumes,
+        )
+
     # ---------------------------------------------------------------
     # REMOVE LIQUID --------------------------------------------------
     # ---------------------------------------------------------------

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -91,7 +91,7 @@ class PRCXI9300Deck(Deck):
     """
 
     def __init__(self, name: str, size_x: float, size_y: float, size_z: float, **kwargs):
-        super().__init__(name, size_x, size_y, size_z)
+        super().__init__(size_x, size_y, size_z, name)
         self.slots = [None] * 16  # PRCXI 9300/9320 最大有 16 个槽位
         self.slot_locations = [Coordinate(0, 0, 0)] * 16
 
@@ -248,14 +248,15 @@ class PRCXI9300TipRack(TipRack):
         if ordered_items is not None:
             items = ordered_items
         elif ordering is not None:
-            # 检查 ordering 中的值是否是字符串（从 JSON 反序列化时的情况）
-            # 如果是字符串，说明这是位置名称，需要让 TipRack 自己创建 Tip 对象
-            # 我们只传递位置信息（键），不传递值，使用 ordering 参数
-            if ordering and isinstance(next(iter(ordering.values()), None), str):
-                # ordering 的值是字符串，只使用键（位置信息）创建新的 OrderedDict
+            # 检查 ordering 中的值类型来决定如何处理：
+            # - 字符串值（从 JSON 反序列化）: 只用键创建 ordering_param
+            # - None 值（从第二次往返序列化）: 同样只用键创建 ordering_param
+            # - 对象值（已经是实际的 Resource 对象）: 直接作为 ordered_items 使用
+            first_val = next(iter(ordering.values()), None) if ordering else None
+            if not ordering or first_val is None or isinstance(first_val, str):
+                # ordering 的值是字符串或 None，只使用键（位置信息）创建新的 OrderedDict
                 # 传递 ordering 参数而不是 ordered_items，让 TipRack 自己创建 Tip 对象
                 items = None
-                # 使用 ordering 参数，只包含位置信息（键）
                 ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
             else:
                 # ordering 的值已经是对象，可以直接使用
@@ -397,14 +398,15 @@ class PRCXI9300TubeRack(TubeRack):
             items_to_pass = ordered_items
             ordering_param = None
         elif ordering is not None:
-            # 检查 ordering 中的值是否是字符串（从 JSON 反序列化时的情况）
-            # 如果是字符串，说明这是位置名称，需要让 TubeRack 自己创建 Tube 对象
-            # 我们只传递位置信息（键），不传递值，使用 ordering 参数
-            if ordering and isinstance(next(iter(ordering.values()), None), str):
-                # ordering 的值是字符串，只使用键（位置信息）创建新的 OrderedDict
+            # 检查 ordering 中的值类型来决定如何处理：
+            # - 字符串值（从 JSON 反序列化）: 只用键创建 ordering_param
+            # - None 值（从第二次往返序列化）: 同样只用键创建 ordering_param
+            # - 对象值（已经是实际的 Resource 对象）: 直接作为 ordered_items 使用
+            first_val = next(iter(ordering.values()), None) if ordering else None
+            if not ordering or first_val is None or isinstance(first_val, str):
+                # ordering 的值是字符串或 None，只使用键（位置信息）创建新的 OrderedDict
                 # 传递 ordering 参数而不是 ordered_items，让 TubeRack 自己创建 Tube 对象
                 items_to_pass = None
-                # 使用 ordering 参数，只包含位置信息（键）
                 ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
             else:
                 # ordering 的值已经是对象，可以直接使用
@@ -595,7 +597,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         return super().set_liquid(wells, liquid_names, volumes)
 
     def set_liquid_from_plate(
-        self, plate: List[ResourceSlot], well_names: list[str], liquid_names: list[str], volumes: list[float]
+        self, plate: ResourceSlot, well_names: list[str], liquid_names: list[str], volumes: list[float]
     ) -> SetLiquidFromPlateReturn:
         return super().set_liquid_from_plate(plate, well_names, liquid_names, volumes)